PLUMED-NEST

Project ID: plumID:20.017
Source: beaded-helix/helix_fisst_fmin-2.0_fmax8.0_eps7.5_10000000.plumed.dat
Originally used with PLUMED version: 2.7
Stable: zipped raw stdout - zipped raw stderr - stderr
Master: zipped raw stdout - zipped raw stderr - stderr

Click on the labels of the actions for more information on what each action computes

#UNITS LENGTH=A TIME=fs ENERGY=kcal/mol

b1The GROUP action with label b1 calculates the following quantities:
 Quantity   
 Type   
 Description  
b1
atoms
indices of atoms specified in GROUP: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=1
b2The GROUP action with label b2 calculates the following quantities:
 Quantity   
 Type   
 Description  
b2
atoms
indices of atoms specified in GROUP: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=12
casThe GROUP action with label cas calculates the following quantities:
 Quantity   
 Type   
 Description  
cas
atoms
indices of atoms specified in GROUP: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=1-12

dendThe DISTANCE action with label dend calculates the following quantities:
 Quantity   
 Type   
 Description  
dend
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=b1,b2
rgThe GYRATION action with label rg calculates the following quantities:
 Quantity   
 Type   
 Description  
rg
scalar
the radius of gyration: GYRATIONCalculate the radius of gyration, or other properties related to it. More details TYPE The type of calculation relative to the Gyration Tensor you want to perform=RADIUS ATOMSthe group of atoms that you are calculating the Gyration Tensor for=cas
enThe ENERGY action with label en calculates the following quantities:
 Quantity   
 Type   
 Description  
en
scalar
the internal energy: ENERGYCalculate the total potential energy of the simulation box. More details 

#The conversion factor is 69.4786 pN = 1 kcal/mol/Angstrom

#0 pN to 100 pN
fThe FISST action with label f calculates the following quantities:
 Quantity   
 Type   
 Description  
f.bias
scalar
the instantaneous value of the bias potential
f.force2
scalar
squared value of force from the bias.
f.dend_fbar
scalar
For each named CV biased, there will be a corresponding output CV_fbar storing the current linear bias prefactor. This particular component measures this quantity for the input CV named dend: FISSTCompute and apply the optimal linear force on an observable to enhance sampling of conformational distributions over a range of applied forces. More details MIN_FORCEMinimum force (per CV) to use for sampling=-2.0 MAX_FORCEMaximum force (per CV) to use for sampling=8.0 PERIODSteps corresponding to the learning rate=200 NINTERPOLATENumber of grid points on which to do interpolation=31 ARGthe labels of the scalars on which the bias will act=dend OUT_RESTARTOutput file for all information needed to continue FISST simulation=helix_fisst_fmin-2.0_fmax8.0_eps7.5_10000000.restart.txt OUT_OBSERVABLEOutput file putting weights needed to compute observables at different force values=helix_fisst_fmin-2.0_fmax8.0_eps7.5_10000000.observable.txt OBSERVABLE_FREQ=1000 CENTER The CV value at which the applied bias energy will be zero=0 KBTThe system temperature in units of KB*T=1

PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=dend,rg,en,f.dend_fbar,f.bias,f.force2 FILEthe name of the file on which to output these quantities=helix_fisst_fmin-2.0_fmax8.0_eps7.5_10000000.en.colvar.txt STRIDE the frequency with which the quantities of interest should be output=5000